Hello Honglan,
It appears that the paths to your data contain some restricted characters.
The only allowed characters when naming paths that are compatible with the
TPP are alpha-numeric and '_' (underscore) ('.' and whitespace are
disallowed.) That doesn't mean that it won't work sometimes when the paths
contain restricted character, but it can be hit or miss. Please rename
the directories and redo analysis.
-David
On Wed, Apr 13, 2016 at 7:40 AM, David Shteynberg <
david.shteynb...@systemsbiology.org> wrote:
> Hi Honglan,
>
> I am on vacation this week. I did fix another processing issue with MSGF+
> earlier, but I was still testing. I will get back to you once I'm back
> next week.
>
> David
> On Apr 13, 2016 12:14 AM, "Honglan Li" <cy0...@gmail.com> wrote:
>
>> Hi David
>>
>> It's me again.
>>
>> Thanks for giving me new PeptideProphet file to run MS_GF+ results.
>>
>> But it still has problem to execute new test file.
>>
>> Would you please tell me the reason?
>>
>>
>> Thanks a lot.
>>
>> Honglan Li
>>
>>
>> XML file:
>> https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing
>>
>> Recieved msg:
>>
>> ----
>> KDModel.cpp, Line 144
>> Expression: idx < posprobs_ -> size()
>>
>> This application has requested the Runtime to terminate it in an unusual
>> way.
>> Please contact the application's support team for more information
>> ----
>>
>> Thanks a lot.
>>
>> Honglan Li
>>
>>
>> 2016년 3월 30일 수요일 오후 8시 30분 5초 UTC+9, Honglan Li 님의 말:
>>>
>>>
>>> Hi David.
>>>
>>> It's me again.
>>>
>>> Last time, you gave me the s/w and cmd.
>>>
>>> It's works well when I use the sample I gave you, and some other XML
>>> files.
>>>
>>> But for some XML files, it still do not work well.
>>>
>>> XML file:
>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing
>>>
>>>
>>> When I executed this test sample (test2.pep.xml.xml) with the cmd you
>>> told me
>>>
>>> "PeptideProphetParser.exe test2.pep.xml.xml NONPARAM
>>> DECOY=XXX DECOYPROBS MINPROB=0 CLEVEL=2 ACCMASS PPM"
>>>
>>> I received msg as follows: (detail: I added captured error msg file)
>>>
>>> ----
>>> KDModel.cpp, Line 144
>>> Expression: idx < posprobs_ -> size()
>>>
>>> This application has requested the Runtime to terminate it in an unusual
>>> way.
>>> Please contact the application's support team for more information
>>> ----
>>>
>>> Would you please tell me what happened to this XML file?
>>>
>>> Thanks a lot.
>>>
>>> Honglan Li
>>>
>>>
>>>
>>> 2016년 3월 28일 월요일 오전 8시 52분 13초 UTC+9, Honglan Li 님의 말:
>>>>
>>>> Thank you very much for your help, David.
>>>>
>>>> It works well now.
>>>>
>>>> Best wishes,
>>>> Honglan Li
>>>>
>>>>
>>>> 2016년 3월 26일 토요일 오전 2시 33분 59초 UTC+9, David Shteynberg 님의 말:
>>>>>
>>>>> Hello Honglan,
>>>>>
>>>>> I was unable to replicate the error on my system, however, I have
>>>>> tested that this command works on a more recently compiled version of
>>>>> PeptideProphet. You can download the binary here
>>>>> https://dl.dropboxusercontent.com/u/21286225/PeptideProphetParser.exe
>>>>> and run as follows
>>>>>
>>>>> PeptideProphetParser.exe test.pep.xml NONPARAM DECOY=XXX DECOYPROBS
>>>>> MINPROB=0 CLEVEL=2 ACCMASS PPM
>>>>>
>>>>>
>>>>> I had to set a fairly high CLEVEL value on this data since MSGF+
>>>>> suffers from scoring highly of some decoys and is not always accurate at
>>>>> the critical 1% error. The WARNING message in the new code has been
>>>>> updated to reflect this problem.
>>>>>
>>>>> Cheers,
>>>>> -David
>>>>>
>>>>>
>>>>> On Thu, Mar 24, 2016 at 8:21 PM, Honglan Li <cy0...@gmail.com> wrote:
>>>>>
>>>>>> Thanks for your quick reply.
>>>>>>>
>>>>>>
>>>>>> I tried the command you told me, but it stll didn't work well.
>>>>>>
>>>>>> The warning msg is "*The discriminant function for MSGFPL is not
>>>>>> yet complete" *
>>>>>>
>>>>>> How to fix it ?
>>>>>>
>>>>>>
>>>>>> *cmd*:
>>>>>>
>>>>>> xinteract -OPd -p0 -dXXX_ *.xml
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Error msg I received*
>>>>>>
>>>>>> ----
>>>>>> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
>>>>>> command completed in 0 sec
>>>>>>
>>>>>> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml'
>>>>>> 'C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>>>>> CYH\uniprot_C+H+Y+48.revCat.fasta'"
>>>>>> - Building Commentz-Walter keyword tree... - Searching the
>>>>>> tree...opening "C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>>>>> CYH\uniprot_C+H+Y+48.revCat.fasta" as
>>>>>> "/home/mllab/hllee/uniprot_C+H+Y+48.revCat.fasta"
>>>>>>
>>>>>> - Linking duplicate entries... - Printing results...
>>>>>>
>>>>>> command completed in 11 sec
>>>>>>
>>>>>> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'
>>>>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_"
>>>>>> Using Decoy Label "XXX_".
>>>>>> Decoy Probabilities will be reported.
>>>>>> Using non-parametric distributions
>>>>>> (MS-GF+) (minprob 0)
>>>>>> WARNING!! *The discriminant function for MSGFPL is not yet complete.*
>>>>>> It is presented here to help facilitate trial and discussion. Reliance
>>>>>> on
>>>>>> this code for publishable scientific results is not recommended.
>>>>>> init with MS-GF+ trypsin
>>>>>> Segmentation fault (core dumped)
>>>>>>
>>>>>> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'
>>>>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" exited with non-zero exit code:
>>>>>> 35584
>>>>>> QUIT - the job is incomplete
>>>>>>
>>>>>> -----
>>>>>>
>>>>>> *XML format per PSM: (file: *
>>>>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3Y2diWDAzVHBQSm8/view?usp=sharing
>>>>>> )
>>>>>>
>>>>>> <spectrum_query
>>>>>> spectrum="C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>>>>> CYH\C-25fmol-R1_QEx2_000090.51174.51174.4" spectrumNativeID="index=51174"
>>>>>> start_scan="51174" end_scan="51174"
>>>>>> precursor_neutral_mass="3972.990669523105" assumed_charge="4" index="1">
>>>>>> <search_result>
>>>>>> <search_hit hit_rank="1"
>>>>>> peptide="VGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPR" peptide_prev_aa="R"
>>>>>> peptide_next_aa="F" protein="sp|P16521|EF3A_YEAST" num_tot_proteins="1"
>>>>>> calc_neutral_pep_mass="3972.99140194498" massdiff="7.32421875e-04"
>>>>>> protein_descr="sp|P16521|EF3A_YEAST Elongation factor 3A OS=Saccharomyces
>>>>>> cerevisiae (strain ATCC 204508 / S288c) GN=YEF3 PE=1 SV=4"
>>>>>> num_tol_term="2"
>>>>>> num_missed_cleavages="1">
>>>>>> <search_score name="raw" value="269"/>
>>>>>> <search_score name="denovo" value="289"/>
>>>>>> <search_score name="SpecEValue"
>>>>>> value="2.8337685502588284E-39"/>
>>>>>> <search_score name="EValue" value="1.2856572993111488E-31"/>
>>>>>> <search_score name="IsotopeError" value="0"/>
>>>>>> </search_hit>
>>>>>> </search_result>
>>>>>> </spectrum_query>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>
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